The first day in the short trial of New Zealand anti-whaling activist Peter Bethune has ended in Tokyo, with a handful of vocal protesters outside the court a sign of the interest that Japan is taking in the case against the member of the militant Sea Shepherd group.

Around 20 Japanese protesters, watched over by police, staged a noisy rally and waved signs saying "Hang terrorist Peter Bethune!" and "Destroy Caucasian discrimination against Japanese!" outside the Tokyo District Court.

Over 400 people queued for the court's 18 seats available to visitors.

Mr Bethune, 45, was the captain of the futuristic powerboat the Ady Gil, which was sliced in two in a collision with the Shonan Maru 2 in the Southern Ocean in January while carrying six crew, and which sank soon after.

The next month he boarded the Japanese ship from a jet ski with the intent of making a citizen's arrest of its captain for the attempted murder of the Ady Gil's crew, and to bill him for the sunken vessel.

Instead, Mr Bethune was detained by the whalers and taken back to Japan, where he was formally arrested by the Japanese Coast Guard on March 12.

He faces a possible 15 years in jail if convicted of five charges including injuring a Japanese whaler with a rancid butter, or butyric acid, stink bomb during a clash in February.

Prosecutors say the projectile caused chemical burns to the face of a 24-year-old crew member, who required one week of medical treatment, and also hurt the eyes of several other whalers.

Mr Bethune also faces a charge of obstructing business, for the group's campaign of harassment, and charges for boarding the security ship on February 15 - trespassing, property destruction and violation of the weapons control law for carrying a knife with a longer-than-legal blade.

"Regarding the assault charge, I deny the charge," he said today.

"For the disruption of business, I admit that I fired the butyric acid but there were additional circumstances that we will discuss in court," he said.

He did not contest the three other charges, Agence France Presse reported.

"For the knife and cutting the net, I admit the fact," he said, referring to cutting a security net in order to enter the ship.

"I admit that I boarded the Shonan Maru 2. But I believe that I had good reason to do so."

His second and third hearings are set for tomorrow and Monday, and a verdict is expected later in June.

Speaking from outside Japan to the Fuji Television Network on Thursday, Sea Shepherd founder Paul Watson said: "I don't think that this is really what you would call justice, it's more of a political trial."

Bethune's father Don, who lives in Hamilton, told NZPA he did not believe his son would be sentenced to the full 15 years, but he could cope if he had to spend time in a Japanese jail.

"He is a remarkable man."

He was disappointed the Japanese had been quicker with bringing their case to court than Maritime New Zealand in even issuing a progress report on its investigation into the collision.

Mr Bethune also slammed the Australian Maritime Safety Authority (AMSA) report, released this month, which failed to find which party was to blame after the Japanese government refused to cooperate - not allowing it to speak to Japanese crew - and Sea Shepherd video footage proved inconclusive.

"There shouldn't be a trial of Pete, there should be a trial of the captain who not only ordered the ramming of a boat a tenth the size of his, in addition to that presumable authorising the firing of the water cannons onto the deck which meant several crew were fighting for their lives."

Commenting on the protesters outside the Tokyo court, Mr Bethune said that with Japan's population of 127 million, it "would not have been too difficult to find 40 or 50 people who felt extremely about the case".

He feared that under the Japanese legal system, prosecutors could decide the accused's fate, and it was rubber-stamped by the judges.

"The Japanese authorities have managed to keep the public in the dark about the actual ramming, mainly by only showing the footage taken from the Shonan Maru."

Prosecutors quoted the Shonan Maru 2 captain Komiya Hiroyuki as saying: "The Sea Shepherd's actions are unforgivable and we would like (the court) to hand down a severe punishment."

The case throws a spotlight on Japanese whaling, which the country defends as part of its culture and carries out under a loophole to an international moratorium that allows lethal "scientific research".